Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 56 of 284
Found at i:19632959 original size:153 final size:152
Alignment explanation
Indices: 19632654--19632956 Score: 565
Period size: 153 Copynumber: 2.0 Consensus size: 152
19632644 CATTTGCCTC
19632654 ATCAAATATCTAATAATACGCACCTTCCACATTGGTCGTTCGGCCACAATATACGCACATCGCCT
1 ATCAAATATCTAATAATACGCACCTTCCACATTGGTCGTTCGGCCACAATATACGCACATCGCCT
*
19632719 ACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATTG
66 ACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA-ATACATATTTCACATTG
19632784 ACCATTCGGCTTTACCACATATG
130 ACCATTCGGCTTTACCACATATG
19632807 ATCAAATATCTAATAATACGCACCTTCCACATTGGTCGTTCGGCCACAATATACGCACATCGCCT
1 ATCAAATATCTAATAATACGCACCTTCCACATTGGTCGTTCGGCCACAATATACGCACATCGCCT
19632872 ACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTC-ATACATATTTCACATT-A
66 ACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCAATACATATTTCACATTGA
19632935 GCCATTCGGCTTTACCACATAT
131 -CCATTCGGCTTTACCACATAT
19632957 ATGCATGTTC
Statistics
Matches: 148, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
150 1 0.01
151 36 0.24
153 111 0.75
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.31
Consensus pattern (152 bp):
ATCAAATATCTAATAATACGCACCTTCCACATTGGTCGTTCGGCCACAATATACGCACATCGCCT
ACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCAATACATATTTCACATTGA
CCATTCGGCTTTACCACATATG
Found at i:19633867 original size:47 final size:47
Alignment explanation
Indices: 19632927--19633851 Score: 1778
Period size: 47 Copynumber: 19.7 Consensus size: 47
19632917 CATACATATT
* * * *
19632927 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
19632974 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633021 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633068 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633115 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633162 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633209 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633256 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633303 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633350 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633397 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633444 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633491 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633538 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633585 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633632 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633679 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633726 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
19633773 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
19633820 TCACATTGGCCATTCGGCCTTATCTCATATAT
1 TCACATTGGCCATTCGGCCTTATCACATATAT
19633852 ACACATTGAC
Statistics
Matches: 867, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 867 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:19639350 original size:19 final size:21
Alignment explanation
Indices: 19639326--19639367 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
19639316 GTTTAGCCTC
19639326 CTCTG-TAC-TTCTACCGATA
1 CTCTGTTACGTTCTACCGATA
*
19639345 CTCTGTTGCGTTCTACCGATA
1 CTCTGTTACGTTCTACCGATA
19639366 CT
1 CT
19639368 AATTGAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (21 bp):
CTCTGTTACGTTCTACCGATA
Found at i:19641289 original size:21 final size:21
Alignment explanation
Indices: 19641265--19641305 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19641255 GAATTAAATG
19641265 AATATACATTTGAAGAATTAC
1 AATATACATTTGAAGAATTAC
* * *
19641286 AATATGCCTTTGATGAATTA
1 AATATACATTTGAAGAATTA
19641306 ACTACAGATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (21 bp):
AATATACATTTGAAGAATTAC
Found at i:19652269 original size:3 final size:3
Alignment explanation
Indices: 19652263--19652314 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
19652253 CTTGTACACG
* *
19652263 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT CTAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
19652308 TAT TAT T
1 TAT TAT T
19652315 TATTTATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:19655533 original size:29 final size:29
Alignment explanation
Indices: 19655481--19655579 Score: 121
Period size: 29 Copynumber: 3.5 Consensus size: 29
19655471 TAGCCCACTT
* *
19655481 GGCCCAA-TCTCATTTATATGGCCCATCA
1 GGCCCAATTCACATTCATATGGCCCATCA
19655509 GGCCCAATTCACATTCATATGGCCCATCA
1 GGCCCAATTCACATTCATATGGCCCATCA
* * * *
19655538 GGCCTAATTCATATTCATGTGGCCCATTA
1 GGCCCAATTCACATTCATATGGCCCATCA
*
19655567 GG-CCAAATCACAT
1 GGCCCAATTCACAT
19655580 GTATATTCAT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
28 15 0.25
29 46 0.75
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (29 bp):
GGCCCAATTCACATTCATATGGCCCATCA
Found at i:19663207 original size:29 final size:29
Alignment explanation
Indices: 19663157--19663262 Score: 142
Period size: 29 Copynumber: 3.7 Consensus size: 29
19663147 TGGCCTACTT
* *
19663157 GGCCCAA-TCTCATTTATATGGCCCATCA
1 GGCCCAATTCACATTCATATGGCCCATCA
19663185 GGCCCAATTCACATTCATATGGCCCATCA
1 GGCCCAATTCACATTCATATGGCCCATCA
* * *
19663214 GGCCCACTTCATATTCATATGGCCCATTA
1 GGCCCAATTCACATTCATATGGCCCATCA
* *
19663243 GGCCCAAATCACATGCATAT
1 GGCCCAATTCACATTCATAT
19663263 TCATGCTCAC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
28 7 0.10
29 61 0.90
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.26
Consensus pattern (29 bp):
GGCCCAATTCACATTCATATGGCCCATCA
Found at i:19664756 original size:16 final size:17
Alignment explanation
Indices: 19664725--19664760 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
19664715 ACAAAGAAAG
*
19664725 TTTAGGATTTCGGGATT
1 TTTAGGATTTCAGGATT
19664742 TTTAGG-TTTCAGGATT
1 TTTAGGATTTCAGGATT
19664758 TTT
1 TTT
19664761 GGGGTGTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.17, C:0.06, G:0.25, T:0.53
Consensus pattern (17 bp):
TTTAGGATTTCAGGATT
Found at i:19673056 original size:25 final size:25
Alignment explanation
Indices: 19673022--19673072 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
19673012 CAAGGAGGTG
*
19673022 TAAACCTTGATATCTGTTAAGGAAA
1 TAAACCTTGATATCGGTTAAGGAAA
19673047 TAAACCTTGATATCGGTTAAGGAAA
1 TAAACCTTGATATCGGTTAAGGAAA
19673072 T
1 T
19673073 TAGTAAGGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (25 bp):
TAAACCTTGATATCGGTTAAGGAAA
Found at i:19674884 original size:9 final size:9
Alignment explanation
Indices: 19674870--19674906 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
19674860 TATAGTTTGA
19674870 TATTCGAAT
1 TATTCGAAT
19674879 TATTCGAAT
1 TATTCGAAT
*
19674888 TATTCGAGT
1 TATTCGAAT
19674897 TATTCGAAT
1 TATTCGAAT
19674906 T
1 T
19674907 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:19674974 original size:9 final size:9
Alignment explanation
Indices: 19674960--19674990 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
19674950 TCGAGTTGAT
19674960 TCGAATAAC
1 TCGAATAAC
19674969 TCGAATAAC
1 TCGAATAAC
19674978 TCGAATAAC
1 TCGAATAAC
19674987 TCGA
1 TCGA
19674991 TTCGTTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (9 bp):
TCGAATAAC
Found at i:19676416 original size:22 final size:21
Alignment explanation
Indices: 19676364--19676418 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
19676354 CTCTCTCCAA
*
19676364 GGTTAGGGCTTTTTATTTTTAT
1 GGTTAGGG-TTTTTATTTTTAG
19676386 GGTTAAGGG-TTTTATTTTATTAG
1 GGTT-AGGGTTTTTA-TTT-TTAG
19676409 GGTTAGGGTT
1 GGTTAGGGTT
19676419 AGGATTTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 5 0.18
22 11 0.39
23 12 0.43
ACGTcount: A:0.16, C:0.02, G:0.29, T:0.53
Consensus pattern (21 bp):
GGTTAGGGTTTTTATTTTTAG
Found at i:19681293 original size:18 final size:18
Alignment explanation
Indices: 19681270--19681304 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19681260 AAGTTACATA
*
19681270 GGCACGGACACGGGCTGG
1 GGCACGGAAACGGGCTGG
19681288 GGCACGGAAACGGGCTG
1 GGCACGGAAACGGGCTG
19681305 AGACACGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.26, G:0.49, T:0.06
Consensus pattern (18 bp):
GGCACGGAAACGGGCTGG
Found at i:19681311 original size:18 final size:18
Alignment explanation
Indices: 19681272--19681311 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19681262 GTTACATAGG
* * *
19681272 CACGGACACGGGCTGGGG
1 CACGGAAACGGGCTGAGA
19681290 CACGGAAACGGGCTGAGA
1 CACGGAAACGGGCTGAGA
19681308 CACG
1 CACG
19681312 ATCGTGTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.42, T:0.05
Consensus pattern (18 bp):
CACGGAAACGGGCTGAGA
Found at i:19683813 original size:28 final size:28
Alignment explanation
Indices: 19683769--19683860 Score: 105
Period size: 28 Copynumber: 3.2 Consensus size: 28
19683759 AAGATATCCT
*
19683769 TTTAACAGAGATAGCCATAAAGGCTTCC
1 TTTAACAGAGATAGCCACAAAGGCTTCC
*
19683797 TTTAACAGATACT-GCCACAAAGGCTTCC
1 TTTAACAGAGA-TAGCCACAAAGGCTTCC
** * *
19683825 TTTAGTAGAGTTAGCCACAAAGGCTCCC
1 TTTAACAGAGATAGCCACAAAGGCTTCC
19683853 TTTTAACA
1 -TTTAACA
19683861 AAACCAGCCA
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
27 1 0.02
28 45 0.87
29 6 0.12
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (28 bp):
TTTAACAGAGATAGCCACAAAGGCTTCC
Found at i:19683826 original size:57 final size:58
Alignment explanation
Indices: 19683765--19683886 Score: 133
Period size: 56 Copynumber: 2.1 Consensus size: 58
19683755 CATAAAGATA
* * * *
19683765 TCCTTTTAACAGAGATAGCCATAAAGGCTTCC-TTTAACAGATA-CTGCCACAAAGGCT
1 TCCTTTTAACAGAGATAGCCACAAAGGCTCCCTTTTAACA-AAACCAGCCACAAAGGCT
** * *
19683822 TCC-TTTAGTAGAGTTAGCCACAAAGGCTCCCTTTTAACAAAACCAGCCACTAAGGCT
1 TCCTTTTAACAGAGATAGCCACAAAGGCTCCCTTTTAACAAAACCAGCCACAAAGGCT
*
19683879 TACTTTTA
1 TCCTTTTA
19683887 TGGAAATTGG
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
56 25 0.47
57 24 0.45
58 4 0.08
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (58 bp):
TCCTTTTAACAGAGATAGCCACAAAGGCTCCCTTTTAACAAAACCAGCCACAAAGGCT
Found at i:19693923 original size:30 final size:31
Alignment explanation
Indices: 19693884--19693943 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
19693874 GGAGGTGGGA
*
19693884 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
19693915 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
19693944 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:19700572 original size:30 final size:30
Alignment explanation
Indices: 19700538--19700617 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 30
19700528 AGCTTCGGGT
19700538 ATCAAATTATGAAAAGGGATGGTAACAACC
1 ATCAAATTATGAAAAGGGATGGTAACAACC
** * *
19700568 ATCAAACAATGAAAAGGGATGGTGACGACC
1 ATCAAATTATGAAAAGGGATGGTAACAACC
*
19700598 ATTAAATTATGAAAAGGGAT
1 ATCAAATTATGAAAAGGGAT
19700618 TGCTTCGATT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (30 bp):
ATCAAATTATGAAAAGGGATGGTAACAACC
Found at i:19719891 original size:19 final size:18
Alignment explanation
Indices: 19719855--19719893 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
19719845 CAAACTACGA
* *
19719855 TATCAAAAACGTAGAAAT
1 TATCAAAAACGAACAAAT
19719873 TATCAAAAACCGAACAAAT
1 TATCAAAAA-CGAACAAAT
19719892 TA
1 TA
19719894 CATACCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.56, C:0.15, G:0.08, T:0.21
Consensus pattern (18 bp):
TATCAAAAACGAACAAAT
Found at i:19720184 original size:21 final size:21
Alignment explanation
Indices: 19720142--19720182 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
19720132 CCATTAAAAG
19720142 AACAAATCAATTTAGCACTTT
1 AACAAATCAATTTAGCACTTT
19720163 AACAAAT-AA-TTAGCAACTTT
1 AACAAATCAATTTAGC-ACTTT
19720183 TACTTTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 7 0.37
21 7 0.37
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32
Consensus pattern (21 bp):
AACAAATCAATTTAGCACTTT
Found at i:19725093 original size:41 final size:39
Alignment explanation
Indices: 19725001--19725195 Score: 138
Period size: 41 Copynumber: 4.7 Consensus size: 39
19724991 TGGTCGGGGG
* * * * *
19725001 TTTTAGTGGCGTTTTTAATCAACCGCCGCTAACGTTAAGGT
1 TTTTAGCGGCGTTTTT-TTGAAGCGCCGCTAATGTT-AGGT
* * * *
19725042 ATTGAACGGCGTTTTCTTTGAAGCGCCGCTAATGTTTGGT
1 TTTTAGCGGCGTTTT-TTTGAAGCGCCGCTAATGTTAGGT
** * *
19725082 CTTTTAGCGGCGTTTTTAAGTAAGCGCCGCTAAAGTTAAGAT
1 -TTTTAGCGGCGTTTTTTTG-AAGCGCCGCTAATGTT-AGGT
* * *
19725124 TTTTAGCGGAGTTTTTTTTGAGAAGAGCCGCTAATGTTAGGGG
1 TTTTAGCGGCG-TTTTTTT--GAAGCGCCGCTAATGTTA-GGT
*
19725167 TTTTAGCGGCATTTTTGTTGAAGCGCCGC
1 TTTTAGCGGCGTTTTT-TTGAAGCGCCGC
19725196 AAAAAACATT
Statistics
Matches: 118, Mismatches: 27, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
40 5 0.04
41 72 0.61
42 14 0.12
43 26 0.22
44 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (39 bp):
TTTTAGCGGCGTTTTTTTGAAGCGCCGCTAATGTTAGGT
Found at i:19725182 original size:84 final size:82
Alignment explanation
Indices: 19724983--19725182 Score: 213
Period size: 82 Copynumber: 2.4 Consensus size: 82
19724973 TTAAGTATTC
** * * *
19724983 GCCGCTAATGGTCGGGGGTTTTAGTGGCGTTTTTAATCAACCGCCGCTAACGTTAAGGTATTGAA
1 GCCGCTAAT-GTTAGGGGTTTTAGCGGCGTTTTTAATCAACCGCCGCTAAAGTTAAGATATTGAA
* *
19725048 CGGCGTTTTCTTTGAAGC
65 CGGAGTTTTCTTTGAAGA
* ** * * * *
19725066 GCCGCTAATGTTTGGTCTTTTAGCGGCGTTTTTAAGT-AAGCGCCGCTAAAGTTAAGATTTTTAG
1 GCCGCTAATGTTAGGGGTTTTAGCGGCGTTTTTAA-TCAACCGCCGCTAAAGTTAAGATATTGAA
*
19725130 CGGAGTTTTTTTTGAGAAGA
65 CGGAGTTTTCTTT--GAAGA
*
19725150 GCCGCTAATGTTAGGGGTTTTAGCGGCATTTTT
1 GCCGCTAATGTTAGGGGTTTTAGCGGCGTTTTT
19725183 GTTGAAGCGC
Statistics
Matches: 96, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
82 53 0.55
83 10 0.10
84 33 0.34
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.36
Consensus pattern (82 bp):
GCCGCTAATGTTAGGGGTTTTAGCGGCGTTTTTAATCAACCGCCGCTAAAGTTAAGATATTGAAC
GGAGTTTTCTTTGAAGA
Found at i:19726120 original size:14 final size:14
Alignment explanation
Indices: 19726102--19726187 Score: 77
Period size: 15 Copynumber: 5.9 Consensus size: 14
19726092 CGGTTAACGT
19726102 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGGG
*
19726116 CTAGGGGTTA-GGG
1 TTAGGGGTTAGGGG
*
19726129 TTAGGGATTTAGGGG
1 TTAGGG-GTTAGGGG
19726144 TTAGTGGGATTTAGGGG
1 TTAG-GGG--TTAGGGG
*
19726161 -TAGGGGTTAGGGAT
1 TTAGGGGTTAGGG-G
*
19726175 TTAGGGTTTAGGG
1 TTAGGGGTTAGGG
19726188 TGTCAAGGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
13 14 0.24
14 12 0.20
15 21 0.36
16 5 0.08
17 7 0.12
ACGTcount: A:0.17, C:0.01, G:0.50, T:0.31
Consensus pattern (14 bp):
TTAGGGGTTAGGGG
Found at i:19726131 original size:6 final size:7
Alignment explanation
Indices: 19726102--19726187 Score: 77
Period size: 7 Copynumber: 11.9 Consensus size: 7
19726092 CGGTTAACGT
19726102 TTAGGGG
1 TTAGGGG
19726109 TTAGGGG
1 TTAGGGG
*
19726116 CTAGGGG
1 TTAGGGG
19726123 TTA-GGG
1 TTAGGGG
*
19726129 TTAGGGAT
1 TTAGGG-G
19726137 TTAGGGG
1 TTAGGGG
19726144 TTAGTGGG
1 TTAG-GGG
19726152 ATTTAGGGG
1 --TTAGGGG
19726161 -TAGGGG
1 TTAGGGG
*
19726167 TTAGGGAT
1 TTAGGG-G
*
19726175 TTAGGGT
1 TTAGGGG
19726182 TTAGGG
1 TTAGGG
19726188 TGTCAAGGGT
Statistics
Matches: 67, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
6 12 0.18
7 33 0.49
8 15 0.22
9 3 0.04
10 4 0.06
ACGTcount: A:0.17, C:0.01, G:0.50, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:19726168 original size:38 final size:35
Alignment explanation
Indices: 19726101--19726187 Score: 113
Period size: 38 Copynumber: 2.4 Consensus size: 35
19726091 GCGGTTAACG
19726101 TTTAGGGGTTAGGGGCTAGGGGTTAGGGTTAGGGA
1 TTTAGGGGTTAGGGGCTAGGGGTTAGGGTTAGGGA
*
19726136 TTTAGGGGTTAGTGGGATTTAGGGG-TAGGGGTTAGGGA
1 TTTAGGGGTTAG-GGG--CTAGGGGTTA-GGGTTAGGGA
*
19726174 TTTAGGGTTTAGGG
1 TTTAGGGGTTAGGG
19726188 TGTCAAGGGT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
35 12 0.26
36 3 0.07
37 4 0.09
38 27 0.59
ACGTcount: A:0.17, C:0.01, G:0.49, T:0.32
Consensus pattern (35 bp):
TTTAGGGGTTAGGGGCTAGGGGTTAGGGTTAGGGA
Found at i:19728066 original size:12 final size:12
Alignment explanation
Indices: 19728049--19728073 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19728039 AGTTTGAAAC
19728049 TGTTCATAATTT
1 TGTTCATAATTT
19728061 TGTTCATAATTT
1 TGTTCATAATTT
19728073 T
1 T
19728074 CACTATCCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TGTTCATAATTT
Found at i:19728128 original size:17 final size:17
Alignment explanation
Indices: 19728102--19728140 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
19728092 ATAGAAAACG
19728102 ATAA-AATGTTAT-TAGA
1 ATAATAATGTTATAT-GA
19728118 ATAATAATGTTATATGA
1 ATAATAATGTTATATGA
19728135 ATAATA
1 ATAATA
19728141 TTATGAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.19
17 16 0.76
18 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (17 bp):
ATAATAATGTTATATGA
Found at i:19728476 original size:26 final size:26
Alignment explanation
Indices: 19728447--19728504 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
19728437 CTCATTGCAT
*
19728447 AATAATTCTTACTCTATAGCTTATCA
1 AATAATTCTTACTCTATAGCTTATAA
*
19728473 AATAATTCTTACTCTGTAGCTTATAA
1 AATAATTCTTACTCTATAGCTTATAA
19728499 AATAAT
1 AATAAT
19728505 ATAAATCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (26 bp):
AATAATTCTTACTCTATAGCTTATAA
Found at i:19739202 original size:42 final size:42
Alignment explanation
Indices: 19739109--19739285 Score: 205
Period size: 42 Copynumber: 4.2 Consensus size: 42
19739099 ACCGACACTT
* * * *
19739109 AGCCTGCTAGACATATAA-TCTGA-AATATTTCACTGGCATTA
1 AGCCTGCTAGACGTA-AAGTCTGATATTGTTTCACCGGCATTA
* *
19739150 AGCCTACTAGACGTAAAGTCTGATATTGTTTCACCGGAATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
* * * *
19739192 AGCTTGCTAGACGTAAAGTCTCAAATTATTTCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
* * *
19739234 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACTGTCAATA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
*
19739276 AGCCAGCTAG
1 AGCCTGCTAG
19739286 GCGCTAAGCC
Statistics
Matches: 114, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
40 2 0.02
41 18 0.16
42 94 0.82
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (42 bp):
AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
Found at i:19739231 original size:84 final size:83
Alignment explanation
Indices: 19739113--19739267 Score: 249
Period size: 84 Copynumber: 1.9 Consensus size: 83
19739103 ACACTTAGCC
* *
19739113 TGCTAGACATATAATCTGAAATATTTCACTGGCATTAAGCCTACTAGACGTAAAGTCTGATATTG
1 TGCTAGACATATAATCTCAAATATTTCACCGGCATTAAGCCTACTAGACGTAAAGTCTGATATTG
19739178 TTTCACCGGAATTAAGCT
66 TTTCACCGGAATTAAGCT
* *
19739196 TGCTAGACGTA-AAGTCTCAAATTATTTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATAT
1 TGCTAGACATATAA-TCTCAAA-TATTTCACCGGCATTAAGCCTACTAGACGTAAAGTCTGATAT
19739260 TGTTTCAC
64 TGTTTCAC
19739268 TGTCAATAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
82 2 0.03
83 16 0.24
84 48 0.73
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (83 bp):
TGCTAGACATATAATCTCAAATATTTCACCGGCATTAAGCCTACTAGACGTAAAGTCTGATATTG
TTTCACCGGAATTAAGCT
Found at i:19739285 original size:84 final size:83
Alignment explanation
Indices: 19739109--19739285 Score: 241
Period size: 84 Copynumber: 2.1 Consensus size: 83
19739099 ACCGACACTT
* *
19739109 AGCCTGCTAGACATATAATCTGAAATATTTCACTGGCATTAAGCCTACTAGACGTAAAGTCTGAT
1 AGCCTGCTAGACATATAATCTCAAATATTTCACCGGCATTAAGCCTACTAGACGTAAAGTCTGAT
*
19739174 ATTGTTTCACCGGAATTA
66 ATTGTTTCACCGCAATTA
* * *
19739192 AGCTTGCTAGACGTA-AAGTCTCAAATTATTTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTG
1 AGCCTGCTAGACATATAA-TCTCAAA-TATTTCACCGGCATTAAGCCTACTAGACGTAAAGTCTG
*
19739256 ATATTGTTTCACTGTCAA-TA
64 ATATTGTTTCACCG-CAATTA
*
19739276 AGCCAGCTAG
1 AGCCTGCTAG
19739286 GCGCTAAGCC
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
82 2 0.02
83 19 0.23
84 59 0.72
85 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (83 bp):
AGCCTGCTAGACATATAATCTCAAATATTTCACCGGCATTAAGCCTACTAGACGTAAAGTCTGAT
ATTGTTTCACCGCAATTA
Found at i:19742451 original size:26 final size:26
Alignment explanation
Indices: 19742415--19742478 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
19742405 AATTTTTCAG
19742415 GTATGTTTTAATCATTTCTTCCATAA
1 GTATGTTTTAATCATTTCTTCCATAA
*
19742441 GTATGTTTTAATCATTTCTTTCATAA
1 GTATGTTTTAATCATTTCTTCCATAA
*
19742467 GTTTGTTTTAAT
1 GTATGTTTTAAT
19742479 AAATGAATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.55
Consensus pattern (26 bp):
GTATGTTTTAATCATTTCTTCCATAA
Found at i:19755509 original size:153 final size:153
Alignment explanation
Indices: 19755231--19755536 Score: 585
Period size: 153 Copynumber: 2.0 Consensus size: 153
19755221 ATGACCCACA
19755231 ACAAACGGGTAGTCCTATACATGCCATTTCGAAGTTCAACCAAAATTGTACCAAAAGGGGGGGGC
1 ACAAACGGGTAGTCCTATACATGCCATTTCGAAGTTCAACCAAAATTGTACCAAAAGGGGGGGGC
*
19755296 TTTGATAGTGTGGGCGACTTCGACTTCAAAATCCCGAGTCCGATAGCTGGAGAACCAAAATCTAT
66 TTTGATAGTGTGGGCGACTTCGACTTCAAAATCCCGAGTCCGATAGCTGGAGAACCAAAATATAT
19755361 AAAACAGAGGATCAAAGAAACGG
131 AAAACAGAGGATCAAAGAAACGG
*
19755384 ACAAACGGGTAGTCCTATACATGCCATTTCGAAGTTCAACCAAAATTGTACCAAAAGTGGGGGGC
1 ACAAACGGGTAGTCCTATACATGCCATTTCGAAGTTCAACCAAAATTGTACCAAAAGGGGGGGGC
*
19755449 TTTGATAGTGTGGGCTACTTCGACTTCAAAATCCCGAGTCCGATAGCTGGAGAACCAAAATATAT
66 TTTGATAGTGTGGGCGACTTCGACTTCAAAATCCCGAGTCCGATAGCTGGAGAACCAAAATATAT
19755514 AAAACAGAGGATCAAAGAAACGG
131 AAAACAGAGGATCAAAGAAACGG
19755537 GGTAAGCAAT
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 150 1.00
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.21
Consensus pattern (153 bp):
ACAAACGGGTAGTCCTATACATGCCATTTCGAAGTTCAACCAAAATTGTACCAAAAGGGGGGGGC
TTTGATAGTGTGGGCGACTTCGACTTCAAAATCCCGAGTCCGATAGCTGGAGAACCAAAATATAT
AAAACAGAGGATCAAAGAAACGG
Found at i:19755998 original size:79 final size:82
Alignment explanation
Indices: 19755887--19756071 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
19755877 GCTACTCGTT
* * *
19755887 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
19755950 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
19755967 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
19756030 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
19756047 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
19756072 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:19756071 original size:40 final size:40
Alignment explanation
Indices: 19755868--19756071 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
19755858 CGGAATTTAA
** *
19755868 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
19755908 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
19755948 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
19755987 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
19756027 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
19756067 CCGGA
1 CCGGA
19756072 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:19762421 original size:42 final size:43
Alignment explanation
Indices: 19762308--19762428 Score: 140
Period size: 42 Copynumber: 2.8 Consensus size: 43
19762298 ACAGTGCTAT
* *
19762308 TCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGATTTAATA
1 TCGGG-CTTCGAACCTAGCAGGCTATAATGCCGGTGAGTTAATA
* *
19762352 -CGAGCTT-TAAGCCTAGCAGGCTATAATGCCGGTGAGTTAATA
1 TCGGGCTTCGAA-CCTAGCAGGCTATAATGCCGGTGAGTTAATA
* * *
19762394 TCGGGCTTCGAACCTAACAGGC-GTAATGCTGGTGA
1 TCGGGCTTCGAACCTAGCAGGCTATAATGCCGGTGA
19762429 ATGAATTCAG
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
41 1 0.02
42 44 0.68
43 18 0.28
44 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (43 bp):
TCGGGCTTCGAACCTAGCAGGCTATAATGCCGGTGAGTTAATA
Found at i:19765615 original size:53 final size:55
Alignment explanation
Indices: 19765524--19765631 Score: 166
Period size: 53 Copynumber: 2.0 Consensus size: 55
19765514 TTATTCATTT
*
19765524 ATTCAACCACGTATTTCTTAGAATGCCTGTTGAACCGTACGTAATTAAATAGGATC
1 ATTCAACCACGTATTTC-TAGAATGCCTGTTGAACCGTACGGAATTAAATAGGATC
* *
19765580 ATTCAACCACGTA-TTC-AGAATGCCTGTTGAGCCGTACGGAATTAAATGGGAT
1 ATTCAACCACGTATTTCTAGAATGCCTGTTGAACCGTACGGAATTAAATAGGAT
19765632 ACACAGATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
53 33 0.67
55 3 0.06
56 13 0.27
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (55 bp):
ATTCAACCACGTATTTCTAGAATGCCTGTTGAACCGTACGGAATTAAATAGGATC
Found at i:19765761 original size:42 final size:43
Alignment explanation
Indices: 19765659--19765771 Score: 138
Period size: 43 Copynumber: 2.7 Consensus size: 43
19765649 AGCTCATACA
* *
19765659 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCAAATATAG
1 ATGCCAATGTCCCAGACATGGTCTTACATGAAATCAAATATAG
** * * * **
19765702 ATGCCTCTATCCTAGACAGGGTCTTACATGAAATTGAATAT-G
1 ATGCCAATGTCCCAGACATGGTCTTACATGAAATCAAATATAG
19765744 ATGCCAATGTCCCAGACATGGTCTTACA
1 ATGCCAATGTCCCAGACATGGTCTTACA
19765772 CGTAAATCTC
Statistics
Matches: 56, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
42 24 0.43
43 32 0.57
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGAAATCAAATATAG
Found at i:19775714 original size:42 final size:43
Alignment explanation
Indices: 19775618--19775787 Score: 141
Period size: 43 Copynumber: 4.0 Consensus size: 43
19775608 AGCTCATACA
* * * *
19775618 ATGCCAACGTCCTAGACATGGTCTTACATGTAATCAAATATAG
1 ATGCCAACGTCCCAGACAGGGTCTTACACGAAATCAAATATAG
* * *
19775661 ATG-CATCTGTCCCAGATAGGGTCTTACACGAAATCGAATA-AG
1 ATGCCAAC-GTCCCAGACAGGGTCTTACACGAAATCAAATATAG
* * * *
19775703 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAA-ATCG
1 ATGCCAACGTCCCAGACAGGGTCTTACACG-AAATC-AAATATAG
* * * *
19775747 ATTCCAACGTCCCAGA-TGTGGTCTTACACGATATCACATAT
1 ATGCCAACGTCCCAGACAG-GGTCTTACACGAAATCAAATAT
19775788 CGAAATCCTA
Statistics
Matches: 100, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
42 29 0.29
43 43 0.43
44 28 0.28
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACACGAAATCAAATATAG
Found at i:19777172 original size:22 final size:20
Alignment explanation
Indices: 19777146--19777186 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
19777136 TTATCAAAGT
19777146 ATTTAAGTTTATTTTCTTTTTC
1 ATTTAAG-TTA-TTTCTTTTTC
*
19777168 ATTTATGTTATTTCTTTTT
1 ATTTAAGTTATTTCTTTTT
19777187 TACAATAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (20 bp):
ATTTAAGTTATTTCTTTTTC
Found at i:19778665 original size:14 final size:15
Alignment explanation
Indices: 19778643--19778672 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
19778633 GAATATTAAA
19778643 ACAAGAATTAAGAAC
1 ACAAGAATTAAGAAC
19778658 ACAA-AATTAAGAAC
1 ACAAGAATTAAGAAC
19778672 A
1 A
19778673 AATCAAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.63, C:0.13, G:0.10, T:0.13
Consensus pattern (15 bp):
ACAAGAATTAAGAAC
Found at i:19781018 original size:20 final size:20
Alignment explanation
Indices: 19780989--19781028 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19780979 CTTCAAGAAT
* *
19780989 AAATATAAATAAAAGTAAAA
1 AAATAAAAATAAAAATAAAA
19781009 AAATAAAAATAAAAATAAAA
1 AAATAAAAATAAAAATAAAA
19781029 CTAGTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (20 bp):
AAATAAAAATAAAAATAAAA
Found at i:19783888 original size:22 final size:22
Alignment explanation
Indices: 19783817--19783891 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
19783807 CATGCATTTG
19783817 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * * **
19783839 TATGATGAATG-TGAACATGTACATA
1 TGTGAT-AAGGCCG-A-ATGGCCA-A
19783864 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
19783886 TGTGAT
1 TGTGAT
19783892 GAATTTGAAC
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 13 0.34
23 9 0.24
24 9 0.24
25 7 0.18
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:19784690 original size:22 final size:22
Alignment explanation
Indices: 19784663--19784737 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
19784653 CATGCATATG
19784663 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
***
19784685 TGTGATGAA-TATGAACAT-GCACATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
19784710 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
19784732 TGTGAT
1 TGTGAT
19784738 CAATGTGAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 14 0.35
23 9 0.22
24 9 0.22
25 8 0.20
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:19784784 original size:22 final size:22
Alignment explanation
Indices: 19784709--19784784 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
19784699 ACATGCACAT
*
19784709 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCAGAATGGCCA
*
19784731 ATGTGATCAATGTG-A-ACAT-GCATA
1 ATGTGAT-AA-G-GCAGA-ATGGC-CA
19784755 TATGTGATAAGGCAGAATGGCCA
1 -ATGTGATAAGGCAGAATGGCCA
19784778 ATGTGAT
1 ATGTGAT
19784785 GAACGTGGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
22 15 0.36
23 10 0.24
24 9 0.21
25 8 0.19
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCAGAATGGCCA
Found at i:19784821 original size:47 final size:47
Alignment explanation
Indices: 19783773--19784787 Score: 1895
Period size: 47 Copynumber: 21.6 Consensus size: 47
19783763 GTATATATGA
* * *
19783773 GATAAGGCCGAATGGCAAATGTGATGAATGTGAACATGCATTTGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
* * * * *
19783820 GATAAGGCCGAATGGCCAATATGATGAATGTGAACATGTACATATGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19783867 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19783914 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19783961 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19784008 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19784055 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19784102 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19784149 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19784196 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19784243 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19784290 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19784337 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19784384 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19784431 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19784478 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19784525 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19784572 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
19784619 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
* * *
19784666 GATAAGGCCGAATGGCCAATGTGATGAATATGAACATGCACATATGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
* * *
19784713 GATAAGGCCGAATGGCCAATGTGATCAATGTGAACATGCATATATGT
1 GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
*
19784760 GATAAGGCAGAATGGCCAATGTGATGAA
1 GATAAGGCCGAATGGCCAATGTGATGAA
19784788 CGTGGAAGTG
Statistics
Matches: 949, Mismatches: 19, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 949 1.00
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.27
Consensus pattern (47 bp):
GATAAGGCCGAATGGCCAATGTGATGAATTTGAACATGCATATGTGT
Found at i:19784854 original size:46 final size:46
Alignment explanation
Indices: 19784801--19784891 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
19784791 GGAAGTGTAT
* * *
19784801 ATATGTGGGAAAGCCGAATGGTTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
* * *
19784847 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATG
19784892 TGTATATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.34, C:0.07, G:0.32, T:0.27
Consensus pattern (46 bp):
ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
Found at i:19797666 original size:30 final size:30
Alignment explanation
Indices: 19797621--19797680 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
19797611 ATTTAATATG
* *
19797621 AACTTTTGCAAAATTACATTTTTGCCCCTA
1 AACTTCTGCAAAATTACACTTTTGCCCCTA
*
19797651 AACTTCTGCATAATTACACTTTTGCCCCTA
1 AACTTCTGCAAAATTACACTTTTGCCCCTA
19797681 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.27, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTCTGCAAAATTACACTTTTGCCCCTA
Found at i:19804066 original size:13 final size:13
Alignment explanation
Indices: 19804048--19804073 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19804038 CAGCTAAACT
19804048 GAAACAGAAGGAA
1 GAAACAGAAGGAA
19804061 GAAACAGAAGGAA
1 GAAACAGAAGGAA
19804074 CAGCTAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.31, T:0.00
Consensus pattern (13 bp):
GAAACAGAAGGAA
Found at i:19804079 original size:36 final size:36
Alignment explanation
Indices: 19804038--19804116 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
19804028 GGTTGTGAAG
*
19804038 CAGCTAAACTGAAACAGAAGGAAGAAACAGAAGGAA
1 CAGCTAAACTGAAACAGAAAGAAGAAACAGAAGGAA
*
19804074 CAGCTAAACTGAAACAGAAAGAAGAAATAGAAGGAA
1 CAGCTAAACTGAAACAGAAAGAAGAAACAGAAGGAA
*
19804110 CGGCTAA
1 CAGCTAA
19804117 GTTGTGAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.54, C:0.14, G:0.24, T:0.08
Consensus pattern (36 bp):
CAGCTAAACTGAAACAGAAAGAAGAAACAGAAGGAA
Found at i:19806179 original size:13 final size:13
Alignment explanation
Indices: 19806161--19806186 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19806151 GGGATTTGTT
19806161 TTAACTAAACTAA
1 TTAACTAAACTAA
19806174 TTAACTAAACTAA
1 TTAACTAAACTAA
19806187 GAATGCACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACTAAACTAA
Found at i:19809268 original size:13 final size:13
Alignment explanation
Indices: 19809250--19809274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19809240 GTAAGTGGTT
19809250 TTGATGATTTTTC
1 TTGATGATTTTTC
19809263 TTGATGATTTTT
1 TTGATGATTTTT
19809275 GTACTTTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TTGATGATTTTTC
Found at i:19810006 original size:47 final size:48
Alignment explanation
Indices: 19809938--19810207 Score: 220
Period size: 47 Copynumber: 5.6 Consensus size: 48
19809928 TTTGTGCGCT
* * *
19809938 AGTGTAAGA-CATGTCTCGGACAT-GTATCAGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCAGACACATTATGAGAGCC
* * * * *
19809984 AGTGTAAGACCATGTTTGGGACAT-GCATC-GGC-C-TTAAGATGTAAGTC
1 AGTGTAAGACCATGTCTAGGACATGGCATCAGACACATTATGA-G--AGCC
**
19810031 AGTGTAAGACCATGTCTAGGACATGGCATC-GACACAGAGATGTAAGAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCAGACACA-TTATG--AGAGCC
* * * *
19810081 AGTGTGAGACCATGTCTAGGACATGGCATCGGTACAAATTTGTGAGAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCAG-ACACA-TTATGAGAGCC
* *
19810131 AGTGTAAGACTATGTCTGGGACATGGCATC--A-AC-TTGATGGATGAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCAGACACATT-AT-GA-GAGCC
19810178 AGTGTAAGACCATGTCTAGGACATGGCATC
1 AGTGTAAGACCATGTCTAGGACATGGCATC
19810208 GAAATTACAC
Statistics
Matches: 183, Mismatches: 26, Indels: 29
0.77 0.11 0.12
Matches are distributed among these distances:
44 7 0.04
45 3 0.02
46 14 0.08
47 75 0.41
48 7 0.04
49 1 0.01
50 65 0.36
51 3 0.02
52 7 0.04
53 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTAGGACATGGCATCAGACACATTATGAGAGCC
Found at i:19810095 original size:50 final size:49
Alignment explanation
Indices: 19809978--19810209 Score: 244
Period size: 50 Copynumber: 4.8 Consensus size: 49
19809968 CCACATTATG
* * *
19809978 AGAGCCAGTGTAAGACCATGTTTGGGACAT-GCATCGGC-CTTAAGATGT-
1 AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACAC--AAGATGTA
*
19810026 A-AGTCAGTGTAAGACCATGTCTAGGACATGGCATCGACACAGAGATGTA
1 AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACACA-AGATGTA
* ** *
19810075 AGAGCCAGTGTGAGACCATGTCTAGGACATGGCATCGGTACA-AATTTGTG
1 AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATC-G-ACACAAGATGTA
* * ** *
19810125 AGAGCCAGTGTAAGACTATGTCTGGGACATGGCATC-A-ACTTGATGGA
1 AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACACAAGATGTA
*
19810172 TGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGA
1 AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGA
19810210 AATTACACCC
Statistics
Matches: 154, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
46 1 0.01
47 62 0.40
48 15 0.10
49 2 0.01
50 69 0.45
51 2 0.01
52 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.23
Consensus pattern (49 bp):
AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACACAAGATGTA
Found at i:19810103 original size:97 final size:97
Alignment explanation
Indices: 19809978--19810208 Score: 272
Period size: 97 Copynumber: 2.4 Consensus size: 97
19809968 CCACATTATG
* * * * *
19809978 AGAGCCAGTGTAAGACCATGTTTGGGACAT-GCATCGG-CCTTAAGATGT-A-AGTCAGTGTAAG
1 AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGTAC-AAAGATGTGAGAGCCAGTGTAAG
*
19810039 ACCATGTCTAGGACATGGCATCGACACAGAGATGTA
65 ACCATGTCTAGGACATGGCATC-A-AC-GAGATGGA
* **
19810075 AGAGCCAGTGTGAGACCATGTCTAGGACATGGCATCGGTACAAATTTGTGAGAGCCAGTGTAAGA
1 AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGTACAAAGATGTGAGAGCCAGTGTAAGA
* * **
19810140 CTATGTCTGGGACATGGCATCAACTTGATGGA
66 CCATGTCTAGGACATGGCATCAACGAGATGGA
*
19810172 TGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCG
1 AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCG
19810209 AAATTACACC
Statistics
Matches: 115, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
97 67 0.58
98 14 0.12
99 3 0.03
100 31 0.27
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (97 bp):
AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGTACAAAGATGTGAGAGCCAGTGTAAGA
CCATGTCTAGGACATGGCATCAACGAGATGGA
Found at i:19816826 original size:13 final size:13
Alignment explanation
Indices: 19816808--19816832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19816798 GTAAGTGATT
19816808 TTGATGATTTTTC
1 TTGATGATTTTTC
19816821 TTGATGATTTTT
1 TTGATGATTTTT
19816833 GCACTTTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TTGATGATTTTTC
Found at i:19817651 original size:46 final size:49
Alignment explanation
Indices: 19817507--19817869 Score: 321
Period size: 46 Copynumber: 7.7 Consensus size: 49
19817497 TTTGTGTGCT
* * * *
19817507 AGTGTAAGA-CATGTCTAGGATAT-GCATCGGCCAC-ATTATG-AGAGCT
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGA-GATGTAGAGCC
* * ** * *
19817553 AGTGTAAGACCATGTCTAGGACATAGTATCGGTATTGAGATG-AGAGCT
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATGTAGAGCC
* *
19817601 AGTGTAAGA-CATGTTTGGGACAT-GCATCGGCCTCGAGATGTA-AGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATGTAGAGCC
* *
19817647 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CTACGAGATGT---GTC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCT-CGAGATGTAGAGCC
* *
19817691 AGTGTAAGACCATGTCTAGGACATGGCATCGGCATGGAGATGTGAGAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATGT-AGAGCC
* * ** * *
19817741 AGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATTTCG-ATAGTC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGAT-GTAGAGCC
* * * *
19817790 AGTGTAAAACCATGTCTAGGACATGGCATC-GACT--TGATGGATGAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATGTA-GAGCC
19817837 AGTGTAAGACCATGTCTAGGACATGGCATCGGC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGC
19817870 ATTACACCCT
Statistics
Matches: 262, Mismatches: 39, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
44 11 0.04
45 16 0.06
46 78 0.30
47 59 0.23
48 28 0.11
49 32 0.12
50 37 0.14
51 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATGTAGAGCC
Found at i:19817852 original size:146 final size:138
Alignment explanation
Indices: 19817507--19817871 Score: 394
Period size: 140 Copynumber: 2.6 Consensus size: 138
19817497 TTTGTGTGCT
* * * * * *
19817507 AGTGTAAGACATGTCTAGGATATGCATCGGCCAC-ATTATGAGAGCTAGTGTAAGACCATGTCTA
1 AGTGTAAAACATGTCTAGGACATGCATCGACTACGA-GAT--GAGCCAGTGTAAGACCATGTCTA
* * * * * *
19817571 GGACATAGTATCGGTATTGAGATGAGAGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCTCG
63 GGACATGGCATCGGCATGGAGATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCG
19817636 AGATGTAAGCC
128 AGATGTAAGCC
* * * * *
19817647 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGTCAGTGTAAGACCATGTCTAGGA
1 AGTGTAAAACATGTCTAGGACATGCATCGACTACGAGATGAGCCAGTGTAAGACCATGTCTAGGA
*
19817712 CATGGCATCGGCATGGAGATGTGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTC
66 CATGGCATCGGCATGGAGA--TGAGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTC
** *
19817777 GATTTCG-ATAGTC
127 GAGAT-GTA-AGCC
*
19817790 AGTGTAAAACCATGTCTAGGACATGGCATCGACT-TGATGGATGAGCCAGTGTAAGACCATGTCT
1 AGTGTAAAA-CATGTCTAGGACAT-GCATCGACTACGA--GATGAGCCAGTGTAAGACCATGTCT
19817854 AGGACATGGCATCGGCAT
62 AGGACATGGCATCGGCAT
19817872 TACACCCTAT
Statistics
Matches: 191, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
138 38 0.20
140 49 0.26
141 14 0.07
142 14 0.07
143 12 0.06
144 15 0.08
145 8 0.04
146 41 0.21
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (138 bp):
AGTGTAAAACATGTCTAGGACATGCATCGACTACGAGATGAGCCAGTGTAAGACCATGTCTAGGA
CATGGCATCGGCATGGAGATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGA
TGTAAGCC
Found at i:19817860 original size:96 final size:96
Alignment explanation
Indices: 19817545--19817869 Score: 307
Period size: 96 Copynumber: 3.4 Consensus size: 96
19817535 GGCCACATTA
* * * * * * *
19817545 TGAGAGCTAGTGTAAGACCATGTCTAGGACATAGTATCGG--TATTGAGATGAGAGCTAGTGTAA
1 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTA-CGAGATGTG-TC-AGTGTAA
* * * * *
19817608 GA-CATGTTTGGGACAT-GCATCGGCCTCGAGATG
63 AACCATGTCTAGGACATGGCATCGACAT-GAGATG
*
19817641 T-A-AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CTACGAGATGTGTCAGTGTAAGAC
1 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTACGAGATGTGTCAGTGTAAAAC
*
19817701 CATGTCTAGGACATGGCATCGGCATGGAGATG
66 CATGTCTAGGACATGGCATCGACAT-GAGATG
* **
19817733 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCT-CGATTTCGATAGTCAGTGTAA
1 TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTACGAGAT-G-T-GTCAGTGTAA
*
19817797 AACCATGTCTAGGACATGGCATCGAC-T-TGATG
63 AACCATGTCTAGGACATGGCATCGACATGAGATG
*
19817829 -GATGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGC
1 TGA-GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
19817870 ATTACACCCT
Statistics
Matches: 199, Mismatches: 18, Indels: 24
0.83 0.07 0.10
Matches are distributed among these distances:
90 9 0.05
91 13 0.07
92 29 0.15
93 16 0.08
94 25 0.13
95 17 0.09
96 51 0.26
97 3 0.02
98 2 0.01
99 34 0.17
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (96 bp):
TGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTACGAGATGTGTCAGTGTAAAAC
CATGTCTAGGACATGGCATCGACATGAGATG
Found at i:19821759 original size:26 final size:26
Alignment explanation
Indices: 19821723--19821776 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
19821713 GGGAGTTAGT
19821723 AAATTTGAAGGAATGAATCATTTTTA
1 AAATTTGAAGGAATGAATCATTTTTA
*
19821749 AAATTTTAAGGAATGAATCATTTTTA
1 AAATTTGAAGGAATGAATCATTTTTA
19821775 AA
1 AA
19821777 GAAACTCTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.39
Consensus pattern (26 bp):
AAATTTGAAGGAATGAATCATTTTTA
Found at i:19822953 original size:11 final size:10
Alignment explanation
Indices: 19822925--19822957 Score: 52
Period size: 9 Copynumber: 3.5 Consensus size: 10
19822915 ATGACAAAAA
19822925 ATATTTTTA-
1 ATATTTTTAT
19822934 ATATTTTTAT
1 ATATTTTTAT
19822944 ATATTTTT-T
1 ATATTTTTAT
19822953 ATATT
1 ATATT
19822958 AAAATACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATATTTTTAT
Found at i:19823351 original size:29 final size:30
Alignment explanation
Indices: 19823292--19823358 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 30
19823282 ACTATCATGA
*
19823292 TAGGTTAACCCAAATTAAAAGTGATCTAAT
1 TAGGTTAGCCCAAATTAAAAGTGATCTAAT
19823322 TAGGTTAGCCCAAATT-AAAGTGATCTAAT
1 TAGGTTAGCCCAAATTAAAAGTGATCTAAT
*
19823351 TTGGTTAG
1 TAGGTTAG
19823359 AATTTTATCG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (30 bp):
TAGGTTAGCCCAAATTAAAAGTGATCTAAT
Found at i:19827342 original size:18 final size:19
Alignment explanation
Indices: 19827313--19827360 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
19827303 AAAAATTCAA
*
19827313 AAAAATTAATAAAGAAT-TT
1 AAAAATT-ATAAAAAATGTT
19827332 AAAAATTATAAAAAATGTT
1 AAAAATTATAAAAAATGTT
19827351 -AAAATTATAA
1 AAAAATTATAA
19827361 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (19 bp):
AAAAATTATAAAAAATGTT
Found at i:19827347 original size:10 final size:10
Alignment explanation
Indices: 19827282--19827347 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 10
19827272 TTTAACAAAC
19827282 TAAAAAA-TA
1 TAAAAAATTA
* *
19827291 TCAAAATTTA
1 TAAAAAATTA
*
19827301 TTAAAAATTCA
1 TAAAAAATT-A
19827312 -AAAAAATTAA
1 TAAAAAATT-A
*
19827322 TAAAGAATT-
1 TAAAAAATTA
19827331 T-AAAAATTA
1 TAAAAAATTA
19827340 TAAAAAAT
1 TAAAAAAT
19827348 GTTAAAATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
8 6 0.14
9 7 0.16
10 23 0.52
11 8 0.18
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:19827492 original size:14 final size:14
Alignment explanation
Indices: 19827473--19827500 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19827463 AAATAATAAA
19827473 AAAATAATTAATTT
1 AAAATAATTAATTT
19827487 AAAATAATTAATTT
1 AAAATAATTAATTT
19827501 TCGATCCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAATAATTAATTT
Found at i:19835130 original size:44 final size:44
Alignment explanation
Indices: 19835000--19835114 Score: 135
Period size: 46 Copynumber: 2.5 Consensus size: 44
19834990 GACAAGTGCT
* * **
19835000 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCCAA-ATGTAAG-C
1 AGTGTAAGACATGTCTGGGACATGCATCAG-CTAAAAGATGT--GTC
19835045 TAGTGTAAGACATGTCTGGGACATGCATCAGCTAAAAGATGTGTC
1 -AGTGTAAGACATGTCTGGGACATGCATCAGCTAAAAGATGTGTC
19835090 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
19835115 GTATCAGTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
44 10 0.16
45 20 0.32
46 32 0.52
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCTAAAAGATGTGTC
Found at i:19836206 original size:41 final size:41
Alignment explanation
Indices: 19836128--19836224 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
19836118 CATGTATTTA
* *
19836128 CACACGGGCCA-GGACACGGGCATGTCATGGTCGTGTGAAG
1 CACACGGGCCAGGGACACGGGCATGTCATGGCCATGTGAAG
* *
19836168 CACACGGGCCAGGGACACGGGCGTGTTATGGCCATGTGAAG
1 CACACGGGCCAGGGACACGGGCATGTCATGGCCATGTGAAG
* *
19836209 CACATGGTCCAGGGAC
1 CACACGGGCCAGGGAC
19836225 GCAAATGTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
40 11 0.22
41 39 0.78
ACGTcount: A:0.23, C:0.26, G:0.37, T:0.14
Consensus pattern (41 bp):
CACACGGGCCAGGGACACGGGCATGTCATGGCCATGTGAAG
Found at i:19836573 original size:22 final size:22
Alignment explanation
Indices: 19836545--19836588 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19836535 AGTTGGATCG
*
19836545 AGTCTGGGTGACTTGTGAATGT
1 AGTCTGGGTAACTTGTGAATGT
19836567 AGTCTGGGTAACTTGTGAATGT
1 AGTCTGGGTAACTTGTGAATGT
19836589 TGTGTGCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.09, G:0.34, T:0.36
Consensus pattern (22 bp):
AGTCTGGGTAACTTGTGAATGT
Found at i:19837752 original size:13 final size:14
Alignment explanation
Indices: 19837719--19837753 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
19837709 ATAATTAAAC
19837719 ATAAAATAAATGAA
1 ATAAAATAAATGAA
*
19837733 ATGAAATAAA-GAA
1 ATAAAATAAATGAA
19837746 ATAAAATA
1 ATAAAATA
19837754 GAAAAAGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (14 bp):
ATAAAATAAATGAA
Found at i:19838652 original size:44 final size:44
Alignment explanation
Indices: 19838603--19838694 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
19838593 TGTTCAGGGA
* * *
19838603 TACTTCGACCTT-AAGTCGATGAGGCACTATAAGTGTCGTACTGT
1 TACTTCGA-CTTCAAGTCAATGAGGCACAATAAGTATCGTACTGT
* **
19838647 TACTTCGACTTCGAGTCAATGAGGCACAATGTGTATCGTACTGT
1 TACTTCGACTTCAAGTCAATGAGGCACAATAAGTATCGTACTGT
19838691 TACT
1 TACT
19838695 GTTACTTCGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 3 0.07
44 38 0.93
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (44 bp):
TACTTCGACTTCAAGTCAATGAGGCACAATAAGTATCGTACTGT
Found at i:19839672 original size:43 final size:43
Alignment explanation
Indices: 19839551--19839678 Score: 168
Period size: 43 Copynumber: 3.0 Consensus size: 43
19839541 AAAATTTGAG
* * * * * *
19839551 GCGTTTGTGGAAAAAGCGCCACTAAAAGTCAAGGCCTTTAGCG
1 GCGTTTGTGGGAAAAGCGACGCTAAAAGTCATGGCTTTTAGCA
*
19839594 GCGCTTGTGGGAAAAGC-ACTGCTAAAAGTCATGGCTTTTAGCA
1 GCGTTTGTGGGAAAAGCGAC-GCTAAAAGTCATGGCTTTTAGCA
*
19839637 GCGTTTGTGGGAAAAGCGACGCTAAAAGTCTTGGCTTTTAGC
1 GCGTTTGTGGGAAAAGCGACGCTAAAAGTCATGGCTTTTAGC
19839679 TGCTCTTTTA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.01
43 71 0.96
44 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (43 bp):
GCGTTTGTGGGAAAAGCGACGCTAAAAGTCATGGCTTTTAGCA
Found at i:19839802 original size:31 final size:32
Alignment explanation
Indices: 19839764--19839836 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
19839754 CATTAAATCA
*
19839764 AACCAAAAA-AAGAAAATATAGCAT-AAAATGC
1 AACCAAAAATAA-AAAATATAGCATAAAAATAC
* *
19839795 AACCAAAAATAACAAATTTAGCATAAAAAATAC
1 AACCAAAAATAAAAAATATAGCAT-AAAAATAC
19839828 AACCAAAAA
1 AACCAAAAA
19839837 CATTAATTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 19 0.53
32 2 0.06
33 15 0.42
ACGTcount: A:0.66, C:0.15, G:0.05, T:0.14
Consensus pattern (32 bp):
AACCAAAAATAAAAAATATAGCATAAAAATAC
Found at i:19840537 original size:13 final size:14
Alignment explanation
Indices: 19840511--19840539 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19840501 ACTAATAACG
19840511 AATTAAACCATTAT
1 AATTAAACCATTAT
19840525 AATTAAA-CATTAT
1 AATTAAACCATTAT
19840538 AA
1 AA
19840540 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:19853455 original size:41 final size:41
Alignment explanation
Indices: 19853378--19853688 Score: 324
Period size: 41 Copynumber: 7.7 Consensus size: 41
19853368 ACTTTTTGCA
* * *
19853378 GCGTTTGGACAAAAAATGCCGCTATTGATCAG-TTTTAGTG
1 GCGTTTGGGCCAAAAACGCCGCTATTGATCAGTTTTTAGTG
* * *
19853418 GCGTTTGGACCAAAAACGCCACTATTGATCAGTTTTTAGTA
1 GCGTTTGGGCCAAAAACGCCGCTATTGATCAGTTTTTAGTG
* * *
19853459 GTG-TTGGGCCAACAACGCCGCTATTTATCAGTTTTTAGTG
1 GCGTTTGGGCCAAAAACGCCGCTATTGATCAGTTTTTAGTG
* * * ** * *
19853499 GTGTTT-GGCTAAAAATGCTACTATTCATAAGTTTTTAGTG
1 GCGTTTGGGCCAAAAACGCCGCTATTGATCAGTTTTTAGTG
* * **
19853539 GCCTTTGGGCCAAAAATGCCAATATTGATCAGTTTTTAGTG
1 GCGTTTGGGCCAAAAACGCCGCTATTGATCAGTTTTTAGTG
* **
19853580 GCGTTTGGGCGAAAAATACCGCTATTGATCTA-TTTTTAGTG
1 GCGTTTGGGCCAAAAACGCCGCTATTGATC-AGTTTTTAGTG
** * *
19853621 GCACTTGGGCGAAAAACGCCGCTATTAATCAGTTTTTAGTG
1 GCGTTTGGGCCAAAAACGCCGCTATTGATCAGTTTTTAGTG
* *
19853662 GTGTTTTGGCCAAAAACGCCGCTATTG
1 GCGTTTGGGCCAAAAACGCCGCTATTG
19853689 CTTAGTCTTT
Statistics
Matches: 226, Mismatches: 40, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
40 96 0.42
41 129 0.57
42 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (41 bp):
GCGTTTGGGCCAAAAACGCCGCTATTGATCAGTTTTTAGTG
Found at i:19855190 original size:43 final size:42
Alignment explanation
Indices: 19855047--19855191 Score: 159
Period size: 42 Copynumber: 3.4 Consensus size: 42
19855037 CAGATAACAG
19855047 GGTCTTACAGGAAATCAAGTACGATGCCAACGTCCCAGACGC
1 GGTCTTACAGGAAATCAAGTACGATGCCAACGTCCCAGACGC
** * * * * **
19855089 TATCTTACATGTAATCAAATATCGATGCC-ACTATCTTAGACAG-
1 GGTCTTACAGGAAATCAAGTA-CGATGCCAAC-GTCCCAGAC-GC
19855132 GGTCTTACAGGAAATCAAGTACGATGCCAACGTCCCAGACGC
1 GGTCTTACAGGAAATCAAGTACGATGCCAACGTCCCAGACGC
*
19855174 GGTCTTACACGTAAATCA
1 GGTCTTACA-GGAAATCA
19855192 TAAATTAATA
Statistics
Matches: 80, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
41 1 0.01
42 40 0.50
43 38 0.47
44 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (42 bp):
GGTCTTACAGGAAATCAAGTACGATGCCAACGTCCCAGACGC
Found at i:19862549 original size:18 final size:18
Alignment explanation
Indices: 19862526--19862564 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
19862516 ATTAAACATA
* *
19862526 AAATAAATGAAATGAAAT
1 AAATAAATAAAATAAAAT
19862544 AAATAAATAAAATAAAAT
1 AAATAAATAAAATAAAAT
19862562 AAA
1 AAA
19862565 GAATAGAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAATAAAATAAAAT
Found at i:19863469 original size:44 final size:44
Alignment explanation
Indices: 19863419--19863506 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
19863409 TTCGACCTTA
* *
19863419 AGTCGATGAGGCACTATAAGTGTCGTACTGTTACT-TTGACTTCG
1 AGTCGATGAGGCACCATAAGTGCCGTACTGTTACTGTT-ACTTCG
* **
19863463 AGTCGATGTGGCACCATGTGTGCCGTACTGTTACTGTTACTTCG
1 AGTCGATGAGGCACCATAAGTGCCGTACTGTTACTGTTACTTCG
19863507 GTTTAATCTG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 36 0.95
45 2 0.05
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.34
Consensus pattern (44 bp):
AGTCGATGAGGCACCATAAGTGCCGTACTGTTACTGTTACTTCG
Found at i:19874685 original size:19 final size:19
Alignment explanation
Indices: 19874661--19874701 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
19874651 CATGGCCACA
19874661 TACAAAATGAATCAAATAT
1 TACAAAATGAATCAAATAT
19874680 TACAAAATGAATCAAATAT
1 TACAAAATGAATCAAATAT
19874699 TAC
1 TAC
19874702 CCTAAGCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (19 bp):
TACAAAATGAATCAAATAT
Found at i:19875021 original size:19 final size:19
Alignment explanation
Indices: 19874997--19875036 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
19874987 TGTGTCATCA
*
19874997 TAAATTCATAGGCATAACT
1 TAAATTCATAGACATAACT
**
19875016 TAAATTTGTAGACATAACT
1 TAAATTCATAGACATAACT
19875035 TA
1 TA
19875037 CACATTTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (19 bp):
TAAATTCATAGACATAACT
Found at i:19876117 original size:29 final size:28
Alignment explanation
Indices: 19876070--19876136 Score: 98
Period size: 29 Copynumber: 2.4 Consensus size: 28
19876060 GTTTGCAGGT
* *
19876070 AAAATATTTTCTGGAAAATGATTTCTGG
1 AAAATAATTTCTGAAAAATGATTTCTGG
19876098 AAAATAATTTCTTGAAAAATGATTTCTGG
1 AAAATAATTTC-TGAAAAATGATTTCTGG
*
19876127 AAAATGATTT
1 AAAATAATTT
19876137 ACTTTTCTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
28 10 0.29
29 25 0.71
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.39
Consensus pattern (28 bp):
AAAATAATTTCTGAAAAATGATTTCTGG
Found at i:19876122 original size:15 final size:14
Alignment explanation
Indices: 19876077--19876136 Score: 93
Period size: 14 Copynumber: 4.2 Consensus size: 14
19876067 GGTAAAATAT
19876077 TTTCTGGAAAATGA
1 TTTCTGGAAAATGA
*
19876091 TTTCTGGAAAATAA
1 TTTCTGGAAAATGA
*
19876105 TTTCTTGAAAAATGA
1 TTTC-TGGAAAATGA
19876120 TTTCTGGAAAATGA
1 TTTCTGGAAAATGA
19876134 TTT
1 TTT
19876137 ACTTTTCTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 29 0.71
15 12 0.29
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (14 bp):
TTTCTGGAAAATGA
Found at i:19876621 original size:22 final size:22
Alignment explanation
Indices: 19876596--19876688 Score: 91
Period size: 22 Copynumber: 4.1 Consensus size: 22
19876586 ATCCAAGTGC
*
19876596 ATAACTAATATTACACCATATG
1 ATAACTAATATTACACCACATG
19876618 ATAACTAATATTACACCACATG
1 ATAACTAATATTACACCACATG
* * **
19876640 ATAACAACAACATT-GTCCA-AGTG
1 ATAAC--TAATATTACACCACA-TG
19876663 CATAACTAATATTACACCACATG
1 -ATAACTAATATTACACCACATG
19876686 ATA
1 ATA
19876689 GCAACAATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
22 35 0.62
23 10 0.18
24 11 0.20
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.27
Consensus pattern (22 bp):
ATAACTAATATTACACCACATG
Found at i:19876642 original size:68 final size:68
Alignment explanation
Indices: 19876558--19876688 Score: 244
Period size: 68 Copynumber: 1.9 Consensus size: 68
19876548 ACATAATTAG
*
19876558 TATTACACCACATGATAACAACAACATTATCCAAGTGCATAACTAATATTACACCATATGATAAC
1 TATTACACCACATGATAACAACAACATTATCCAAGTGCATAACTAATATTACACCACATGATAAC
19876623 TAA
66 TAA
*
19876626 TATTACACCACATGATAACAACAACATTGTCCAAGTGCATAACTAATATTACACCACATGATA
1 TATTACACCACATGATAACAACAACATTATCCAAGTGCATAACTAATATTACACCACATGATA
19876689 GCAACAATTT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (68 bp):
TATTACACCACATGATAACAACAACATTATCCAAGTGCATAACTAATATTACACCACATGATAAC
TAA
Found at i:19876671 original size:46 final size:46
Alignment explanation
Indices: 19876618--19876730 Score: 199
Period size: 46 Copynumber: 2.5 Consensus size: 46
19876608 ACACCATATG
19876618 ATAACTAATATTACACCACATGATAACAACAACATTGTCCAAGTGC
1 ATAACTAATATTACACCACATGATAACAACAACATTGTCCAAGTGC
* **
19876664 ATAACTAATATTACACCACATGATAGCAACAATTTTGTCCAAGTGC
1 ATAACTAATATTACACCACATGATAACAACAACATTGTCCAAGTGC
19876710 ATAACTAATATTACACCACAT
1 ATAACTAATATTACACCACAT
19876731 TAAAAGTATC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (46 bp):
ATAACTAATATTACACCACATGATAACAACAACATTGTCCAAGTGC
Found at i:19877748 original size:27 final size:30
Alignment explanation
Indices: 19877682--19877754 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 30
19877672 GTCAATCATT
*
19877682 TCAATATCCAACAAGCTTAAAACATAATAAAC
1 TCAATATCTAACAAGCTTAAAAC--AATAAAC
*
19877714 TCAATATCTAACAAGCTTGAAAC-AT-AA-
1 TCAATATCTAACAAGCTTAAAACAATAAAC
19877741 TCAATATCTAACAA
1 TCAATATCTAACAA
19877755 AATCAAGACA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 14 0.36
28 2 0.05
29 2 0.05
32 21 0.54
ACGTcount: A:0.51, C:0.21, G:0.04, T:0.25
Consensus pattern (30 bp):
TCAATATCTAACAAGCTTAAAACAATAAAC
Found at i:19879284 original size:15 final size:15
Alignment explanation
Indices: 19879264--19879292 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19879254 TTCTCAAGTA
19879264 ATGACTAAAGTTACC
1 ATGACTAAAGTTACC
19879279 ATGACTAAAGTTAC
1 ATGACTAAAGTTAC
19879293 ACTTATACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (15 bp):
ATGACTAAAGTTACC
Found at i:19885658 original size:22 final size:22
Alignment explanation
Indices: 19885632--19885683 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
19885622 AAATGAAAAT
19885632 GAAAATGAAATTGGAATACTTA
1 GAAAATGAAATTGGAATACTTA
19885654 GAAAATGAAATTGGAATACTTA
1 GAAAATGAAATTGGAATACTTA
*
19885676 TAAAATGA
1 GAAAATGA
19885684 TGGAAGAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.52, C:0.04, G:0.17, T:0.27
Consensus pattern (22 bp):
GAAAATGAAATTGGAATACTTA
Found at i:19897367 original size:13 final size:12
Alignment explanation
Indices: 19897300--19897368 Score: 59
Period size: 13 Copynumber: 5.3 Consensus size: 12
19897290 AATTTTAAAC
19897300 AAACTTTTTCAA
1 AAACTTTTTCAA
* *
19897312 AAAGTATTTCTTAA
1 AAACT-TTT-TCAA
19897326 AATCACTTTTTCAA
1 AA--ACTTTTTCAA
19897340 AATACTTTTT-AA
1 AA-ACTTTTTCAA
19897352 AAACTCTTTTCAA
1 AAACT-TTTTCAA
19897365 AAAC
1 AAAC
19897369 AATGTTAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
11 3 0.07
12 12 0.26
13 16 0.35
14 10 0.22
15 3 0.07
16 2 0.04
ACGTcount: A:0.42, C:0.16, G:0.01, T:0.41
Consensus pattern (12 bp):
AAACTTTTTCAA
Found at i:19905978 original size:16 final size:16
Alignment explanation
Indices: 19905957--19905990 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19905947 CCAATATCCA
* *
19905957 ATTATCATATTTGCAC
1 ATTATCACATTTACAC
19905973 ATTATCACATTTACAC
1 ATTATCACATTTACAC
19905989 AT
1 AT
19905991 ATATATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTATCACATTTACAC
Found at i:19906778 original size:4 final size:4
Alignment explanation
Indices: 19906769--19906810 Score: 59
Period size: 4 Copynumber: 10.2 Consensus size: 4
19906759 TGTGCTTCTG
19906769 TTTC TTTC TTTC TTTC TCTT- TTTC TTTC TTTC TTTTC TTTC T
1 TTTC TTTC TTTC TTTC T-TTC TTTC TTTC TTTC -TTTC TTTC T
19906811 AATTTTGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 2 0.06
4 27 0.77
5 6 0.17
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:19906794 original size:20 final size:19
Alignment explanation
Indices: 19906764--19906808 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
19906754 TAGACTGTGC
*
19906764 TTCTGTTTCTTTCTTTCTT
1 TTCTTTTTCTTTCTTTCTT
19906783 TCTCTTTTTCTTTCTTTCTT
1 T-TCTTTTTCTTTCTTTCTT
19906803 TTCTTT
1 TTCTTT
19906809 CTAATTTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (19 bp):
TTCTTTTTCTTTCTTTCTT
Found at i:19911421 original size:16 final size:16
Alignment explanation
Indices: 19911400--19911433 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19911390 CCAATATCCA
* *
19911400 ATTATCATATTTTCAC
1 ATTATCACATTTACAC
19911416 ATTATCACATTTACAC
1 ATTATCACATTTACAC
19911432 AT
1 AT
19911434 ATATATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTATCACATTTACAC
Found at i:19911489 original size:20 final size:19
Alignment explanation
Indices: 19911459--19911499 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
19911449 ATATATATAC
19911459 ATCAATTTAATCCAATTCA
1 ATCAATTTAATCCAATTCA
*
19911478 ATCAACTTTAATTCAATTCA
1 ATCAA-TTTAATCCAATTCA
19911498 AT
1 AT
19911500 ATCAAAGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (19 bp):
ATCAATTTAATCCAATTCA
Found at i:19911675 original size:80 final size:80
Alignment explanation
Indices: 19911588--19911746 Score: 300
Period size: 80 Copynumber: 2.0 Consensus size: 80
19911578 ACCTCAACCA
19911588 CTTACCATATACATTAAATCCAAATACAACAATTAACAATTAGATTCGGATTATATAAATACAAA
1 CTTACCATATACATTAAATCCAAATACAACAATTAACAATTAGATTCGGATTATATAAATACAAA
*
19911653 CCAGAAATTTTGAGT
66 CCAGAAATTCTGAGT
*
19911668 CTTACCATATACATTAAATCCAAATACAATAATTAACAATTAGATTCGGATTATATAAATACAAA
1 CTTACCATATACATTAAATCCAAATACAACAATTAACAATTAGATTCGGATTATATAAATACAAA
19911733 CCAGAAATTCTGAG
66 CCAGAAATTCTGAG
19911747 CTATTCAACG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.30
Consensus pattern (80 bp):
CTTACCATATACATTAAATCCAAATACAACAATTAACAATTAGATTCGGATTATATAAATACAAA
CCAGAAATTCTGAGT
Found at i:19912321 original size:9 final size:9
Alignment explanation
Indices: 19912304--19912337 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
19912294 GGTTCTTACC
19912304 TTCTTTCTT
1 TTCTTTCTT
*
19912313 TTTTTTC-T
1 TTCTTTCTT
19912321 TTCTTTCTT
1 TTCTTTCTT
19912330 TTCTTTCT
1 TTCTTTCT
19912338 AATTTGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTCTTTCTT
Found at i:19912322 original size:13 final size:13
Alignment explanation
Indices: 19912304--19912337 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
19912294 GGTTCTTACC
*
19912304 TTCTTTCTTTTTT
1 TTCTTTCTTTCTT
19912317 TTCTTTCTTTCTT
1 TTCTTTCTTTCTT
19912330 TTCTTTCT
1 TTCTTTCT
19912338 AATTTGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTTCTTTCTT
Found at i:19912326 original size:17 final size:17
Alignment explanation
Indices: 19912304--19912337 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19912294 GGTTCTTACC
*
19912304 TTCTTTCTTTTTTTTCT
1 TTCTTTCTTTTCTTTCT
19912321 TTCTTTCTTTTCTTTCT
1 TTCTTTCTTTTCTTTCT
19912338 AATTTGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTCTTTCTTTTCTTTCT
Found at i:19919469 original size:2 final size:2
Alignment explanation
Indices: 19919464--19920219 Score: 1512
Period size: 2 Copynumber: 378.0 Consensus size: 2
19919454 GATATATATA
19919464 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19919506 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19919548 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19919590 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19919632 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19919674 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19919716 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19919758 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19919800 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19919842 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19919884 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19919926 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19919968 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19920010 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19920052 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19920094 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19920136 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19920178 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
19920220 CAAGTGCCAT
Statistics
Matches: 754, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 754 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:19924541 original size:6 final size:6
Alignment explanation
Indices: 19924524--19924569 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
19924514 GGATAAAAAG
* *
19924524 GATGAT GATGGT GGTGGT GATGGT GATGGT GATGGT GATGGT GATG
1 GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATGGT GATG
19924570 AACTTGACTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
GATGGT
Found at i:19926781 original size:17 final size:17
Alignment explanation
Indices: 19926761--19926795 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19926751 TTAAAATTAA
19926761 AATT-AAAATATAAATAT
1 AATTAAAAATA-AAATAT
19926778 AATTAAAAATAAAATAT
1 AATTAAAAATAAAATAT
19926795 A
1 A
19926796 TATATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTAAAAATAAAATAT
Found at i:19926785 original size:23 final size:23
Alignment explanation
Indices: 19926728--19926800 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
19926718 ACAATTTGAA
* *
19926728 AAATATAATAAAAATT-AATTAT
1 AAATATAATTAAAATTAAAATAT
* *
19926750 -ATTAAAATTAAAATTAAAATAT
1 AAATATAATTAAAATTAAAATAT
*
19926772 AAATATAATTAAAAATAAAATAT
1 AAATATAATTAAAATTAAAATAT
*
19926795 ATATAT
1 AAATAT
19926801 TTATTATATA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
21 12 0.29
22 5 0.12
23 24 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATATAATTAAAATTAAAATAT
Found at i:19929116 original size:57 final size:56
Alignment explanation
Indices: 19929027--19929141 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 56
19929017 GTACAACGTA
19929027 TCTTTCCCACTCTTTGAACATTCCTAATAATTCACAGGGCAGGCGCCTACACTTAC
1 TCTTTCCCACTCTTTGAACATTCCTAATAATTCACAGGGCAGGCGCCTACACTTAC
* * * *
19929083 TNCTTTCCCTCTCTTTGAACTTTCCTAATAATTCACAGGGCAGGCGGCTGCACTTAC
1 T-CTTTCCCACTCTTTGAACATTCCTAATAATTCACAGGGCAGGCGCCTACACTTAC
19929140 TC
1 TC
19929142 AGTCAAGTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 2 0.04
57 52 0.96
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.32
Consensus pattern (56 bp):
TCTTTCCCACTCTTTGAACATTCCTAATAATTCACAGGGCAGGCGCCTACACTTAC
Found at i:19932888 original size:16 final size:16
Alignment explanation
Indices: 19932867--19932908 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
19932857 ATTTTACGAT
19932867 TTTTAAAATGTTTATA
1 TTTTAAAATGTTTATA
*
19932883 TTTT-AAAT-TTTATT
1 TTTTAAAATGTTTATA
19932897 TATTTAAAATGT
1 T-TTTAAAATGT
19932909 CAGTTATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 6 0.27
15 7 0.32
16 8 0.36
17 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (16 bp):
TTTTAAAATGTTTATA
Found at i:19932965 original size:23 final size:23
Alignment explanation
Indices: 19932938--19932982 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
19932928 GTTTGGAATT
* * *
19932938 AAAATTTTATAAATTAAAAATAA
1 AAAATATTAAAAATAAAAAATAA
19932961 AAAATATTAAAAATAAAAAATA
1 AAAATATTAAAAATAAAAAATA
19932983 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAATATTAAAAATAAAAAATAA
Found at i:19932969 original size:16 final size:16
Alignment explanation
Indices: 19932950--19932989 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
19932940 AATTTTATAA
19932950 ATTAAAAATAAAAAAT
1 ATTAAAAATAAAAAAT
19932966 ATTAAAAATAAAAAAT
1 ATTAAAAATAAAAAAT
19932982 ATTAAAAA
1 ATTAAAAA
19932990 ATTAATATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
ATTAAAAATAAAAAAT
Found at i:19943938 original size:41 final size:41
Alignment explanation
Indices: 19943860--19944068 Score: 206
Period size: 41 Copynumber: 5.1 Consensus size: 41
19943850 TACCTAAAAT
*
19943860 AATACACCGGCACGAAGCCTGCTAGGCTCAAGGCCTGATAC
1 AATACACCGGCACGAAGCCTGCTAGGCTCAAGACCTGATAC
* * * *
19943901 AACACACTGGCATGAAGCCTGCTAGGCTTAAGACCTGATAC
1 AATACACCGGCACGAAGCCTGCTAGGCTCAAGACCTGATAC
* *
19943942 AATACACCAGCACAAAGCCTGCTAGGCTCAA-AGCCTGATAC
1 AATACACCGGCACGAAGCCTGCTAGGCTCAAGA-CCTGATAC
* * * * * *
19943983 AATACACCGACAAGATGCCTACTAGGCTCAA-AGCCTGTTAT
1 AATACACCGGCACGAAGCCTGCTAGGCTCAAGA-CCTGATAC
** ** * * *
19944024 GGTACACTTGCTCGAAGCCTGCTTGGCTCAAGACCCGATAC
1 AATACACCGGCACGAAGCCTGCTAGGCTCAAGACCTGATAC
19944065 AATA
1 AATA
19944069 TCTCCAGTAT
Statistics
Matches: 132, Mismatches: 34, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
40 1 0.01
41 130 0.98
42 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.19
Consensus pattern (41 bp):
AATACACCGGCACGAAGCCTGCTAGGCTCAAGACCTGATAC
Found at i:19946242 original size:31 final size:31
Alignment explanation
Indices: 19946207--19946270 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
19946197 AAGCTCATTG
*
19946207 TCGAGTTTGTCTCTACTTAACAAATGACCCT
1 TCGAGTTTGTCTCTACTCAACAAATGACCCT
19946238 TCGAGTTTGTCTCTACTCAACAAATGACCCT
1 TCGAGTTTGTCTCTACTCAACAAATGACCCT
19946269 TC
1 TC
19946271 ATATCTTCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.34
Consensus pattern (31 bp):
TCGAGTTTGTCTCTACTCAACAAATGACCCT
Found at i:19951986 original size:5 final size:5
Alignment explanation
Indices: 19951976--19952004 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
19951966 GTAAGTTAAA
19951976 CGCAC CGCAC CGCAC CGCAC CGCAC CGCA
1 CGCAC CGCAC CGCAC CGCAC CGCAC CGCA
19952005 GTCAATCGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.59, G:0.21, T:0.00
Consensus pattern (5 bp):
CGCAC
Found at i:19959951 original size:18 final size:19
Alignment explanation
Indices: 19959917--19959953 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19959907 TAGCTACGGA
19959917 ATTAAAACAATTAAAATTT
1 ATTAAAACAATTAAAATTT
*
19959936 ATTAATACAA-TAAAATTT
1 ATTAAAACAATTAAAATTT
19959954 CAATTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTAAAACAATTAAAATTT
Found at i:19959973 original size:7 final size:7
Alignment explanation
Indices: 19959961--19959986 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19959951 TTTCAATTTC
19959961 ATATTGA
1 ATATTGA
19959968 ATATTGA
1 ATATTGA
19959975 ATATTGA
1 ATATTGA
19959982 ATATT
1 ATATT
19959987 TAAATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (7 bp):
ATATTGA
Found at i:19960415 original size:4 final size:4
Alignment explanation
Indices: 19960398--19960442 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
19960388 CCATGTGTGA
19960398 CTTT CTTT -TCTT CTTT CTTT C-TT -TTT CTTT CTTT CTTTT CTTT CT
1 CTTT CTTT CT-TT CTTT CTTT CTTT CTTT CTTT CTTT C-TTT CTTT CT
19960443 AATTTGTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
3 5 0.14
4 26 0.72
5 5 0.14
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
CTTT
Found at i:19960427 original size:14 final size:14
Alignment explanation
Indices: 19960398--19960442 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
19960388 CCATGTGTGA
19960398 CTTTCTTTTCTTCTTT
1 CTTTC-TTT-TTCTTT
19960414 CTTTCTTTTTCTTT
1 CTTTCTTTTTCTTT
19960428 CTTTC-TTTTCTTT
1 CTTTCTTTTTCTTT
19960441 CT
1 CT
19960443 AATTTGTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.34
14 11 0.38
15 3 0.10
16 5 0.17
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
CTTTCTTTTTCTTT
Found at i:19960504 original size:18 final size:20
Alignment explanation
Indices: 19960483--19960526 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
19960473 TTTTTTTTTG
19960483 TTATAC-TAACTT-TTATTA
1 TTATACTTAACTTATTATTA
*
19960501 TTATACTTTAATTTATTATTA
1 TTATAC-TTAACTTATTATTA
19960522 TTATA
1 TTATA
19960527 ATATATATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
20 5 0.23
21 11 0.50
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATACTTAACTTATTATTA
Found at i:19965733 original size:12 final size:12
Alignment explanation
Indices: 19965716--19965746 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19965706 GAAGCATGGG
19965716 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
19965728 AGAAAAAGGGAA
1 AGAAAAAGAGAA
19965740 AGAAAAA
1 AGAAAAA
19965747 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:19966617 original size:41 final size:41
Alignment explanation
Indices: 19966572--19966676 Score: 101
Period size: 38 Copynumber: 2.6 Consensus size: 41
19966562 TAACCTCGAG
*
19966572 TCGATGAGACACTGGGTGTCACTATTTTACTTCGGATAAAT
1 TCGATGAGACACTGGGTGTCACTATTTTACTTCGGATAAAC
** * * * * *
19966613 TCGATGAGGTACT-AG-GT-ACCACTTTACTTCGGCTAAGC
1 TCGATGAGACACTGGGTGTCACTATTTTACTTCGGATAAAC
19966651 T-GATGAGACACTGGGTGTCAACTATT
1 TCGATGAGACACTGGGTGTC-ACTATT
19966677 GATTCGAACT
Statistics
Matches: 47, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
37 9 0.19
38 18 0.38
39 4 0.09
40 1 0.02
41 15 0.32
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (41 bp):
TCGATGAGACACTGGGTGTCACTATTTTACTTCGGATAAAC
Found at i:19985082 original size:15 final size:16
Alignment explanation
Indices: 19985036--19985082 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
19985026 TATAAAAATC
*
19985036 ATATATAAAACCTTAAT
1 ATATATAAAA-ATTAAT
19985053 ATATATGAAATAATTAA-
1 ATATAT-AAA-AATTAAT
19985070 ATATATAAAAATT
1 ATATATAAAAATT
19985083 CAAAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.15
16 3 0.11
17 12 0.44
18 7 0.26
19 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (16 bp):
ATATATAAAAATTAAT
Found at i:19987057 original size:31 final size:31
Alignment explanation
Indices: 19987022--19987102 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
19987012 ATGTTTACAC
*
19987022 TTTCATTTTAGTCACTCAACCTTTAGGACGA
1 TTTCATTTTAGTCACCCAACCTTTAGGACGA
* *
19987053 TTTCATTTTAGTCACCCAACTTTTAGGTCGA
1 TTTCATTTTAGTCACCCAACCTTTAGGACGA
*
19987084 TTTCATTTTGGTCACCCAA
1 TTTCATTTTAGTCACCCAA
19987103 AAAATATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.41
Consensus pattern (31 bp):
TTTCATTTTAGTCACCCAACCTTTAGGACGA
Found at i:20004573 original size:146 final size:146
Alignment explanation
Indices: 20004309--20004602 Score: 543
Period size: 146 Copynumber: 2.0 Consensus size: 146
20004299 GTATATACAA
*
20004309 TTGTATATCAAAAGATAACCTCAAACACAACTTATCAATTCATCAAATCCACACTTAATCAATGC
1 TTGTATATCAAAAGATAACCTCAAACACAACTTATCAATTCATCAAATCCACACTTAACCAATGC
* *
20004374 ACCTATCATAGGTACCTCAAATACACATATCATTAACACATACCATTTCTATTTGCATTGAAATA
66 ACCTATCATAGGCACCTCAAATACACATATCATTAACACATACCATTTATATTTGCATTGAAATA
20004439 TCTACCTCATTCACAT
131 TCTACCTCATTCACAT
* *
20004455 TTGTATATCAAAATATAACCTCAAACACAACTTATCAATTCATCAAATCCACACTTAACCAATGT
1 TTGTATATCAAAAGATAACCTCAAACACAACTTATCAATTCATCAAATCCACACTTAACCAATGC
20004520 ACCTATCATAGGCACCTCAAATACACATATCATTAACACATACCATTTATATTTGCATTGAAATA
66 ACCTATCATAGGCACCTCAAATACACATATCATTAACACATACCATTTATATTTGCATTGAAATA
20004585 TCTACCTCATTCACAT
131 TCTACCTCATTCACAT
20004601 TT
1 TT
20004603 ATCTTAAGGT
Statistics
Matches: 143, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
146 143 1.00
ACGTcount: A:0.39, C:0.25, G:0.04, T:0.31
Consensus pattern (146 bp):
TTGTATATCAAAAGATAACCTCAAACACAACTTATCAATTCATCAAATCCACACTTAACCAATGC
ACCTATCATAGGCACCTCAAATACACATATCATTAACACATACCATTTATATTTGCATTGAAATA
TCTACCTCATTCACAT
Found at i:20008169 original size:14 final size:14
Alignment explanation
Indices: 20008150--20008177 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20008140 GACATGTAAA
20008150 TGTCATCTTTTCTT
1 TGTCATCTTTTCTT
20008164 TGTCATCTTTTCTT
1 TGTCATCTTTTCTT
20008178 GGTCCTCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.07, T:0.64
Consensus pattern (14 bp):
TGTCATCTTTTCTT
Found at i:20008756 original size:31 final size:32
Alignment explanation
Indices: 20008710--20008779 Score: 115
Period size: 31 Copynumber: 2.2 Consensus size: 32
20008700 ACCACTGGTA
*
20008710 AAGTGTTCCCATCACCTAAGGAGGCATACTCT
1 AAGTGTTCCCATCACCTAAGAAGGCATACTCT
*
20008742 AAGTGTT-CCATCACCTAAGAAGGCATACTTT
1 AAGTGTTCCCATCACCTAAGAAGGCATACTCT
20008773 AAGTGTT
1 AAGTGTT
20008780 TCAGTAACGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 29 0.81
32 7 0.19
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (32 bp):
AAGTGTTCCCATCACCTAAGAAGGCATACTCT
Done.